JacobPorter
I'm a data scientist and bioinformatics specialist. I have a PhD in computer science from Virginia Tech. My research concerned DNA sequencing technology.
Virginia
Pinned Repositories
AlignmentML
Using machine learning to assess read alignment quality.
app_service
Application execution service.
BFAST-Gap
BFAST-Gap is a modification of the BFAST short DNA read mapper. BFAST-Gap adds functionality for Ion Torrent DNA reads.
BisPin
BisPin is a Python 2.7 program that uses BFAST to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.
bvbrc_metacats
bvbrc_predict_platform
BVBRC module for predicting the sequencing platform
FastNeighborNet
Fast implementations of the Neighbor Net phylogenetic split network method.
InfoTrim
A DNA read quality trimmer using entropy created with Python
PorterTools
PorterTools is a collection of Python 2.7 scripts for processing biological sequence data that have been developed over the course of my research. They are provided for reference.
Simple_Estimator
A simple script that runs assorted sci-kit learn estimators and Bayesian optimization hyperparameter tuning with skopt.
JacobPorter's Repositories
JacobPorter/github-actions-rust-example
Build and test a Rust Project
JacobPorter/rust-mlops-template
A work in progress to build out solutions in Rust for MLOPs
JacobPorter/mlops-template
mlops template
JacobPorter/config
Some configuration files.
JacobPorter/predict_platform
Predict sequencing platform.
JacobPorter/p3_msa
JacobPorter/bvbrc_website
Repository for the BV-BRC website.
JacobPorter/homology_service
JacobPorter/bvbrc_variation
BV-BRC variation computation service
JacobPorter/bvbrc_metacats
JacobPorter/p3_fqutils
JacobPorter/bvbrc_predict_platform
BVBRC module for predicting the sequencing platform
JacobPorter/bvbrc_rnaseq
JacobPorter/minimap_tools
Minimap tools
JacobPorter/p3_core
Core library modules & scripts for PATRIC API integration
JacobPorter/comparative_systems
Scripts for comparative subsystems, pathways
JacobPorter/p3_tnseq
JacobPorter/transit
Repository for the TRANSIT and TPP tools developed by the Ioerger Lab
JacobPorter/Meta-CATS
Metadata-driven Comparative Analysis Tool for Sequences (meta-CATS): an Automated Process for Identifying Significant Sequence Variations that Correlate with Virus Attributes
JacobPorter/p3_web
JacobPorter/SeqIterator
An iterator that can read and write fasta, fastq, and SAM files.
JacobPorter/p3_msa_orig
MSA variance service
JacobPorter/MSAUtil
MSA utilities
JacobPorter/Radogest
JacobPorter/p3_fqutils_original
JacobPorter/app_service
Application execution service.
JacobPorter/Simple_Estimator
A simple script that runs assorted sci-kit learn estimators and Bayesian optimization hyperparameter tuning with skopt.
JacobPorter/AlignmentML
Using machine learning to assess read alignment quality.
JacobPorter/BisPin
BisPin is a Python 2.7 program that uses BFAST to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.
JacobPorter/BFAST-Gap
BFAST-Gap is a modification of the BFAST short DNA read mapper. BFAST-Gap adds functionality for Ion Torrent DNA reads.